TB-Profiler result

Run: SRR1140625
Summary

Run ID: SRR1140625

Sample name:

Date: 02-04-2023 20:57:06

Number of reads: 2433789

Percentage reads mapped: 93.91

Strain: lineage3

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin
katG 2155700 p.Asn138His missense_variant 1.0 isoniazid
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761292 p.Val496Met missense_variant 0.97
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460914 c.-131G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472007 n.162G>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.2
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.24
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.41
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.43
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.43
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.21
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.19
rrl 1473856 n.199A>G non_coding_transcript_exon_variant 0.1
rrl 1474302 n.645G>T non_coding_transcript_exon_variant 0.17
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 0.14
rrl 1475469 n.1812C>T non_coding_transcript_exon_variant 0.14
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.17
rrl 1475479 n.1822C>A non_coding_transcript_exon_variant 0.17
rrl 1475481 n.1824C>A non_coding_transcript_exon_variant 0.17
rrl 1475484 n.1828delC non_coding_transcript_exon_variant 0.15
rrl 1475498 n.1841C>G non_coding_transcript_exon_variant 0.1
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.24
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.43
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918067 p.Ala43Asp missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168605 p.Pro670Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726117 c.-76T>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4240732 p.Asn290Lys missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0